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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ), 'gf_id' => 'HOM05D001413', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001413' ), 'data_identifier' => 'HOM05D001413', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001413', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '444', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p24730' => 'bna', 'A06p05930' => 'bna', 'A06p18320' => 'bna', 'A06p28210' => 'bna', 'A09p01890' => 'bna', 'Aa31LG4G17970' => 'aar', 'Aa31LG5G2070' => 'aar', 'Aa31sc55G120' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.574' => 'aag', 'Actinidia08693' => 'ach', 'Actinidia19776' => 'ach', 'Actinidia24346' => 'ach', 'Actinidia24826' => 'ach', 'Actinidia28280' => 'ach', 'Ah.04g161180' => 'amhyb', 'Ah.07g204790' => 'amhyb', 'Ah.08g213070' => 'amhyb', 'Ah.15g093250' => 'amhyb', 'AL1G12240' => 'aly', 'AL1G19580' => 'aly', 'AL5G29180' => 'aly', 'AL6G50640' => 'aly', 'Aqoxy2G02953' => 'aox', 'Aqoxy5G00749' => 'aox', 'Aqoxy5G04337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ADX0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6QLZ34' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DYK1KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2B8GP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QCFS18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJW25F' => 'arhy', 'AT1G02840' => 'ath', 'AT1G09140' => 'ath', 'AT3G49430' => 'ath', 'AT4G02430' => 'ath', 'ATR0304G063' => 'atr', 'ATR0561G195' => 'atr', 'Atru.chr12.2409' => 'acertr', 'Atru.chr2.76' => 'acertr', 'Atru.chr5.1153' => 'acertr', 'AUR62000755' => 'cqu', 'AUR62004558' => 'cqu', 'AUR62005166' => 'cqu', 'AUR62005213' => 'cqu', 'AUR62006011' => 'cqu', 'AUR62008637' => 'cqu', 'AUR62022674' => 'cqu', 'AUR62033136' => 'cqu', 'AUR62035615' => 'cqu', 'BcaB01g00713' => 'bca', 'BcaB01g02042' => 'bca', 'BcaB02g09589' => 'bca', 'BcaB05g23631' => 'bca', 'BcaB07g34127' => 'bca', 'BcaC01g02407' => 'bca', 'BcaC03g16125' => 'bca', 'BcaC03g16126' => 'bca', 'BcaC05g24765' => 'bca', 'BcaC07g39407' => 'bca', 'BcaNung04053' => 'bca', 'BcaNung05001' => 'bca', 'BolC2t09914H' => 'bol', 'BolC3t18813H' => 'bol', 'BolC5t29468H' => 'bol', 'BolC8t50064H' => 'bol', 'BolC9t53129H' => 'bol', 'BraA02t07460Z' => 'bra', 'BraA06t23800Z' => 'bra', 'BraA06t24915Z' => 'bra', 'BraA06t25763Z' => 'bra', 'BraA09t35840Z' => 'bra', 'C02p39020' => 'bna', 'C03p65600' => 'bna', 'C05p07130' => 'bna', 'C08p24460' => 'bna', 'C09p01970' => 'bna', 'CANSAT21G0820' => 'cansat', 'CANSAT25G2342' => 'cansat', 'CARHR002180' => 'chi', 'CARHR009010' => 'chi', 'CARHR158390' => 'chi', 'CARHR250700' => 'chi', 'Carub.0001s0196' => 'cru', 'Carub.0001s0843' => 'cru', 'Carub.0005s1564' => 'cru', 'Carub.0006s3470' => 'cru', 'Ca_06434_v3' => 'car', 'Ca_09156_v3' => 'car', 'Ca_10134_v3' => 'car', 'CBR_g12769' => 'cbr', 'CBR_g40433' => 'cbr', 'CBR_g72806' => 'cbr', 'Cc01_g20780' => 'ccan', 'Cc01_g20790' => 'ccan', 'Cc02_g00870' => 'ccan', 'Cc02_g31210' => 'ccan', 'Cc02_g31220' => 'ccan', 'Cc02_g34210' => 'ccan', 'CDE02G4376' => 'cde', 'CDE08G0409' => 'cde', 'Cfa005920' => 'cfa', 'Cfa006635' => 'cfa', 'Ciclev10002007m.g' => 'ccl', 'Ciclev10021646m.g' => 'ccl', 'Ciclev10021764m.g' => 'ccl', 'CiPaw.07G022100' => 'cil', 'CiPaw.07G108100' => 'cil', 'CiPaw.08G095600' => 'cil', 'CiPaw.15G130800' => 'cil', 'CiPaw.16G086100' => 'cil', 'ClCG01G000100' => 'cla', 'ClCG03G017320' => 'cla', 'ClCG09G005890' => 'cla', 'COL.COLO4_10528' => 'col', 'COL.COLO4_14363' => 'col', 'COL.COLO4_17893' => 'col', 'COL.COLO4_23353' => 'col', 'Cpa.g.sc19.278' => 'cpa', 'Cpa.g.sc327.5' => 'cpa', 'Cpa.g.sc501.1' => 'cpa', 'Cre01.g026450' => 'cre', 'Cre06.g278239' => 'cre', 'CsaV3_1G038750' => 'csa', 'CsaV3_5G000070' => 'csa', 'CsaV3_7G029260' => 'csa', 'CSS0000532' => 'camsi', 'CSS0000616' => 'camsi', 'CSS0005488' => 'camsi', 'CSS0013176' => 'camsi', 'CSS0016573' => 'camsi', 'CSS0032059' => 'camsi', 'CSS0041647' => 'camsi', 'CSS0045111' => 'camsi', 'CSS0047802' => 'camsi', 'DCAR_008980' => 'dca', 'DCAR_012395' => 'dca', 'DCAR_014562' => 'dca', 'DCAR_018340' => 'dca', 'DCAR_020367' => 'dca', 'DCAR_029392' => 'dca', 'Dinv19698' => 'din', 'Dinv30820' => 'din', 'Dinv32643' => 'din', 'Dinv33052' => 'din', 'Dinv35379' => 'din', 'Dinv40333' => 'din', 'Dinv43554' => 'din', 'Duzib052G0998' => 'dzi', 'Duzib084G1343' => 'dzi', 'Duzib128G0472' => 'dzi', 'Duzib133G0003' => 'dzi', 'Duzib177G0318' => 'dzi', 'Duzib211G0006' => 'dzi', 'ECA232G0007' => 'eca', 'ECA234G1495' => 'eca', 'ECA236G1537' => 'eca', 'ECA236G2979' => 'eca', 'ECA248G3363' => 'eca', 'EL10Ac1g00189' => 'bvu', 'EL10Ac3g05187' => 'bvu', 'EL10Ac4g09907' => 'bvu', 'EL10Ac7g17497' => 'bvu', 'Eucgr.A01412' => 'egr', 'Eucgr.B01911' => 'egr', 'Eucgr.H04537' => 'egr', 'Eucgr.K03474' => 'egr', 'FAN01G0064' => 'fan', 'FAN02G3041' => 'fan', 'FAN03G2828' => 'fan', 'FAN05G2602' => 'fan', 'FAN09G4056' => 'fan', 'FAN10G1183' => 'fan', 'FAN10G2582' => 'fan', 'FAN14G5666' => 'fan', 'FAN20G1601' => 'fan', 'FAN24G0529' => 'fan', 'FvH4_2g25670' => 'fve', 'FvH4_6g06650' => 'fve', 'FvH4_7g32850' => 'fve', 'Glyma.03G214400' => 'gma', 'Glyma.04G229300' => 'gma', 'Glyma.06G135500' => 'gma', 'Glyma.19G211100' => 'gma', 'Glyma.20G236800' => 'gma', 'Gohir.A01G177200' => 'ghi', 'Gohir.A09G186500' => 'ghi', 'Gohir.A11G016400' => 'ghi', 'Gohir.A11G114700' => 'ghi', 'Gohir.A13G109900' => 'ghi', 'Gohir.A13G174500' => 'ghi', 'Gohir.D01G168200' => 'ghi', 'Gohir.D09G181400' => 'ghi', 'Gohir.D10G097700' => 'ghi', 'Gohir.D11G016200' => 'ghi', 'Gohir.D11G119800' => 'ghi', 'Gohir.D13G112500' => 'ghi', 'Gohir.D13G180300' => 'ghi', 'Gorai.002G208700' => 'gra', 'Gorai.006G203400' => 'gra', 'Gorai.007G017000' => 'gra', 'Gorai.007G128300' => 'gra', 'Gorai.011G107200' => 'gra', 'Gorai.013G126300' => 'gra', 'Gorai.013G205700' => 'gra', 'GSVIVG01027997001' => 'vvi', 'GSVIVG01031132001' => 'vvi', 'GSVIVG01038636001' => 'vvi', 'HanXRQChr01g0026641' => 'han', 'HanXRQChr02g0042501' => 'han', 'HanXRQChr04g0100781' => 'han', 'HanXRQChr06g0163811' => 'han', 'HanXRQChr09g0250731' => 'han', 'HanXRQChr10g0299291' => 'han', 'HanXRQChr10g0299301' => 'han', 'HanXRQChr12g0382721' => 'han', 'HanXRQChr15g0485371' => 'han', 'HanXRQChr16g0519221' => 'han', 'Haze_00286' => 'cav', 'Haze_04133' => 'cav', 'Haze_04929' => 'cav', 'Haze_04930' => 'cav', 'Hma1.2p1_0415F.1_g148150' => 'hma', 'Hma1.2p1_1471F.1_g285710' => 'hma', 'HPP92_007251' => 'vpl', 'HPP92_011377' => 'vpl', 'HPP92_014599' => 'vpl', 'Hund05422' => 'sun', 'Hund21715' => 'sun', 'Hund27151' => 'sun', 'Lalb_Chr02g0143251' => 'lal', 'Lalb_Chr04g0260661' => 'lal', 'Lalb_Chr08g0239721' => 'lal', 'Lalb_Chr18g0047011' => 'lal', 'Lalb_Chr21g0306841' => 'lal', 'Lalb_Chr23g0271901' => 'lal', 'Lj1C26G3' => 'lonja', 'Lj1g0006120' => 'lja', 'Lj1g0012156' => 'lja', 'Lj1g0022657' => 'lja', 'Lj2A1193T38' => 'lonja', 'Lj2g0027128' => 'lja', 'Lj3C896T8' => 'lonja', 'Lj5A394G29' => 'lonja', 'Lj5A395T41' => 'lonja', 'Lj5C389G3' => 'lonja', 'Lj5g0006745' => 'lja', 'Lju9216A0T8' => 'lonja', 'Lsat_1_v5_gn_5_146660' => 'lsa', 'Lsat_1_v5_gn_5_191120' => 'lsa', 'Lsat_1_v5_gn_8_53720' => 'lsa', 'Lsat_1_v5_gn_9_50101' => 'lsa', 'Manes.01G042800' => 'mes', 'Manes.01G218300' => 'mes', 'Manes.05G062400' => 'mes', 'Manes.09G171000' => 'mes', 'Mapoly0009s0024' => 'mpo', 'Mapoly0017s0004' => 'mpo', 'MapolyY_A0024' => 'mpo', 'MBI12_g20128_MAGBIO' => 'mbi', 'MBI19_g25351_MAGBIO' => 'mbi', 'MD01G1227800' => 'mdo', 'MD01G1227900' => 'mdo', 'MD03G1287500' => 'mdo', 'MD04G1199500' => 'mdo', 'MD07G1175700' => 'mdo', 'MD07G1298400' => 'mdo', 'MD11G1310700' => 'mdo', 'MD12G1212300' => 'mdo', 'MD12G1261000' => 'mdo', 'MD15G1346900' => 'mdo', 'MD16G1239200' => 'mdo', 'Medtr1g083400' => 'mtr', 'Medtr1g088180' => 'mtr', 'Medtr3g092580' => 'mtr', 'Medtr7g108810' => 'mtr', 'Medtr7g112760' => 'mtr', 'Medtr8g058530' => 'mtr', 'MELO3C015299.2' => 'cme', 'MELO3C016002.2' => 'cme', 'MELO3C033837.2' => 'cme', 'Migut.D00212' => 'egut', 'Migut.F00993' => 'egut', 'Migut.H02128' => 'egut', 'Migut.N01505' => 'egut', 'MSTRG.20408' => 'ama', 'MSTRG.33' => 'ama', 'MSTRG.8543' => 'ama', 'Nitab4.5_0000011g0330' => 'nta', 'Nitab4.5_0000041g0030' => 'nta', 'Nitab4.5_0000319g0180' => 'nta', 'Nitab4.5_0001098g0010' => 'nta', 'Nitab4.5_0001879g0030' => 'nta', 'Nitab4.5_0002470g0090' => 'nta', 'Nitab4.5_0003985g0010' => 'nta', 'Nitab4.5_0005805g0080' => 'nta', 'Nitab4.5_0008207g0020' => 'nta', 'Nitab4.5_0009582g0020' => 'nta', 'Nitab4.5_0010216g0010' => 'nta', 'Nitab4.5_0011192g0010' => 'nta', 'Nitab4.5_0011192g0020' => 'nta', 'Nn1g00431' => 'nnu', 'Nn3g18869' => 'nnu', 'Nn3g21471' => 'nnu', 'Nn3g21473' => 'nnu', 'Oeu007808.1' => 'oeu', 'Oeu010675.2' => 'oeu', 'Oeu023684.3' => 'oeu', 'Oeu043341.1' => 'oeu', 'Oeu048340.1' => 'oeu', 'Oeu055385.2' => 'oeu', 'Os01g0316600' => 'osa', 'Os03g0344100' => 'osa', 'Os05g0364600' => 'osa', 'Os07g0673500' => 'osa', 'Peaxi162Scf00001g00451' => 'pax', 'Peaxi162Scf00037g01329' => 'pax', 'Peaxi162Scf00300g00842' => 'pax', 'Peaxi162Scf00300g00843' => 'pax', 'Peaxi162Scf00399g00922' => 'pax', 'Peaxi162Scf00542g00514' => 'pax', 'PGR042G1124' => 'pgr', 'PGR044G2059' => 'pgr', 'PGR083G2148' => 'pgr', 'PGSC0003DMG400003218' => 'stu', 'PGSC0003DMG400011402' => 'stu', 'PGSC0003DMG400014645' => 'stu', 'PGSC0003DMG400024759' => 'stu', 'Phvul.001G207100' => 'pvu', 'Phvul.007G197400' => 'pvu', 'Phvul.009G046000' => 'pvu', 'Potri.002G205025' => 'ptr', 'Potri.005G024600' => 'ptr', 'Potri.012G021800' => 'ptr', 'Potri.013G015500' => 'ptr', 'Potri.014G129900' => 'ptr', 'Potri.015G004600' => 'ptr', 'Pp3c17_17620' => 'ppa', 'Pp3c1_35700' => 'ppa', 'Pp3c2_2470' => 'ppa', 'PRCOL_00001235' => 'pco', 'PRCOL_00001695' => 'pco', 'Prupe.2G318200' => 'ppe', 'Prupe.6G320000' => 'ppe', 'Prupe.8G260600' => 'ppe', 'Psat3g022160' => 'psa', 'Psat5g072520' => 'psa', 'Psat6g150760' => 'psa', 'PSO063G0079' => 'pso', 'PSO210G4195' => 'pso', 'PSO210G6841' => 'pso', 'PSO782G3403' => 'pso', 'QL03p020105' => 'qlo', 'QL09p007253' => 'qlo', 'QL12p028557' => 'qlo', 'RcHm_v2.0_Chr1g0382791' => 'rch', 'RcHm_v2.0_Chr3g0455851' => 'rch', 'RcHm_v2.0_Chr6g0293931' => 'rch', 'Rhsim01G0284700' => 'rsi', 'Rhsim07G0190000' => 'rsi', 'Rhsim09G0209400' => 'rsi', 'Rhsim13G0010500' => 'rsi', 'Rhsim13G0010600' => 'rsi', 'Sabra02G0154300' => 'sbr', 'Sabra02G0154400' => 'sbr', 'Sabra05G0139400' => 'sbr', 'Sabra12G0011900' => 'sbr', 'Sabra13G0013600' => 'sbr', 'Sabra13G0017700' => 'sbr', 'Sabra14G0096500' => 'sbr', 'Sabra15G0003200' => 'sbr', 'Sc05g0003900' => 'sci', 'Sc09g0002930' => 'sci', 'Sc13g0010230' => 'sci', 'Sc18g0003990' => 'sci', 'Sed0001749' => 'sed', 'Sed0009132' => 'sed', 'Sed0010001' => 'sed', 'Sed0014141' => 'sed', 'Sed0028034' => 'sed', 'SEGI_09981' => 'sgi', 'SEGI_12774' => 'sgi', 'SEGI_12888' => 'sgi', 'SEGI_15460' => 'sgi', 'SEGI_24998' => 'sgi', 'SEGI_27201' => 'sgi', 'SEGI_29420' => 'sgi', 'SEGI_30271' => 'sgi', 'SEGI_36279' => 'sgi', 'SEGI_37821' => 'sgi', 'SGA_v2.0_scaffold141G35559' => 'sas', 'SGA_v2.0_scaffold1G00371' => 'sas', 'SGA_v2.0_scaffold2G01397' => 'sas', 'SGA_v2.0_scaffold459G51952' => 'sas', 'SGA_v2.0_scaffold4G01939' => 'sas', 'SHI19782' => 'shi', 'SMO134G0058' => 'smo', 'SMO202G0078' => 'smo', 'Solyc01g099810.3' => 'sly', 'Solyc03g082380.4' => 'sly', 'Solyc06g009060.4' => 'sly', 'Solyc09g075090.1' => 'sly', 'Sopen01g043320' => 'spe', 'Sopen03g022110' => 'spe', 'Sopen06g003860' => 'spe', 'Sopen09g029910' => 'spe', 'Sp1g01820' => 'spa', 'Sp1g07720' => 'spa', 'Sp6g02340' => 'spa', 'TAR365G0061' => 'tar', 'TAR370G0009' => 'tar', 'TAR374G1589' => 'tar', 'TAR633G0922' => 'tar', 'TAR636G3268' => 'tar', 'THA.LOC104798982' => 'tha', 'THA.LOC104825971' => 'tha', 'Thecc.01G299600' => 'tca', 'Thecc.02G041000' => 'tca', 'Thecc.03G207800' => 'tca', 'Thecc.05G313700' => 'tca', 'Thhalv10008203m.g' => 'esa', 'Thhalv10008507m.g' => 'esa', 'Thhalv10010586m.g' => 'esa', 'Thhalv10028867m.g' => 'esa', 'TPR.G15242' => 'tpr', 'TPR.G17731' => 'tpr', 'TPR.G25093' => 'tpr', 'TPR.G33185' => 'tpr', 'TWI14G0199' => 'twi', 'TWI14G0715' => 'twi', 'TWI23G1288' => 'twi', 'TWI39G0553' => 'twi', 'TWI56G1438' => 'twi', 'unitig_21.g20283' => 'ugi', 'unitig_744.g24489' => 'ugi', 'vmacro02453' => 'vma', 'vmacro04691' => 'vma', 'vmacro10155' => 'vma', 'vmacro14278' => 'vma', 'vmacro15005' => 'vma', 'VMungo1309G1655' => 'vmu', 'VMungo1383G0638' => 'vmu', 'Zm00001eb130650' => 'zma', 'Zm00001eb285560' => 'zma', 'Zm00001eb394920' => 'zma' ) $gf_id = 'HOM05D001413' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001413' ) $data_identifier = 'HOM05D001413' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 6, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 10, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394920' $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